Genomic DNA was extracted from overnight cultures using the
DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA). Sequencing libraries were prepared with either the
TruSeq DNA Sample Prep Kit (Illumina, San Diego, CA, USA) or the
Nextera DNA Sample Prep Kit (Illumina). DNAs were sequenced on the Illumina
MiSeq Platform, generating paired-end 250 bp reads in sufficient quantity to provide over 35X coverage for each genome. Raw reads were trimmed and draft genome sequences were assembled
de novo with CLC Genomics Workbench v6.5.1 or v7.0.4 (CLC bio, Boston, MA, USA). In most cases the entire phage harboring
stx was contained on one contig; otherwise two contigs were bioinformatically joined to obtain the entire phage sequence and this was then verified by mapping the reads onto the phage sequence.
The
stx-encoding prophage sequences were extracted from the genomic assemblies of the strains investigated and aligned to the ΦPOC-J13 phage reference sequence (GenBank accession KJ603229) using the Mauve algorithm within the
MegAlign Pro module of the Lasergene software package (DNASTAR Inc., Madison, WI, USA). Phylogenetic analysis of identified single nucleotide polymorphisms (SNPs) was conducted with SplitsTree 4 [19 (
link)], using the neighbor-net algorithm and untransformed
p distances.
Gray M.D., Lacher D.W., Leonard S.R., Abbott J., Zhao S., Lampel K.A., Prothery E., Gouali M., Weill F.X, & Maurelli A.T. (2015). Prevalence of Stx-producing Shigella species isolated from French Travelers Returning from the Caribbean: An Emerging Pathogen with International Implications. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 21(8), 765.e9-765.e14.
